1. Technical Field
This invention relates to the field of medical sciences, in particular the field of immunology and viral immunity. Specifically, the invention relates to cellular epitopes of the VP1 polypeptide of polyomaviruses, for example BK virus, JC virus and SV40.
2. Description of the Background Art
Polyomavirus hominis 1, known as BK virus (BKV), is a ubiquitous human polyomavirus that causes asymptomatic primary infection and resides, latent, in several body sites, notably the kidney and genitourinary tract. See Stolt et al., J. Gen. Virol. 84:1499-1504, 2003. BKV, the related polyomavirus hominis 2 (also known as JC virus or JCV) and simian vacuolating virus 40 (SV40) are closely related species of the genus polyomavirus. The BKV genome is about 75% homologous overall to JCV and about 70% homologous overall to SV40.
Primary BKV infection during childhood is presumed to occur via the respiratory tract. Following infection, hematologous dissemination is postulated to occur. Persistence is preferentially within the genitourinary tract (renal epithelial cells and the lower genitourinary tract (bladder, ureters)). Chesters et al., J. Infect. Dis. 147:676-684, 1983. BKV reactivation often occurs in immunocompromised individuals such as hematopoietic stem cell transplant and kidney transplant recipients, causing clinical disease states which include hemorrhagic cystitis, ureteric stenosis and polyomavirus-associated nephropathy (PVAN, also referred to as BK virus-associated nephropathy (BKVN)). The incidence of polyomavirus-associated nephropathy, variously reported as between 1% and 8% of kidney transplant patients, has increased in recent years, concomitant with the use of newer and more potent immunosuppressive agents in transplant patients, suggesting that immune responses to BKV are important in control of the virus. Hirsch and Steiger, Lancet 3:611-623, 2003.
Polyomavirus associated nephropathy now is recognized as an important cause of allograft dysfunction in kidney transplant recipients. Binet et al., Transplantation 678:918-922, 1999; Hurault et al., Transplant Proc. 32:2760-2761, 2000; Randawa et al., Transplantation 67:103-109, 1999. With immunosuppression, viral reactivation can occur, presumably primarily from the lower genitourinary tract, and is detected as virus shed in the urine (viruria). With continued immunosuppression and other local injury within the kidney, such as rejection or calcineurin inhibitor toxicity, polyomavirus reactivation also can occur in the kidney itself, leading to viral replication, direct injury to the infected tubular epithelial cells and indirect injury manifested by inflammation and nephritis, ultimately leading to rejection of the kidney in some cases. In kidney transplant recipients, BKV reactivation is particularly associated with interstitial nephritis/nephropathy and ureteric stenosis. Nickeleit et al., J. Am. Soc. Nephrol. 10:1080-1089, 1999; Nickeleit et al., Nephrol. Dial. Transplant. 15:324-332, 2000.
Other than the antiviral agent, cidofovir, for treatment of PVAN, no other antiviral therapies are available for polyomavirus. Kadambi et al., Am. J. Transplant. 3:186-191, 2003; Scantlebury et al., Graft 5(supp):S82-S87, 2002; Vats et al., Transplantation 75:105-112, 2003. Cidofovir requires intravenous administration and is associated with considerable nephrotoxicity itself, particularly in patients with pre-existing nephrotoxicity. Based on a consensus opinion that PVAN may represent a state of relative over-immunosuppression, the current approach to managing patients with PVAN is reduction of immunosuppression. Even using this approach, however, up to 30-50% of patients with PVAN develop progressive polyomavirus infection and deterioration of kidney function, ultimately resulting in loss of the kidney allograft. Hirsch and Steiger, Lancet 3:611-623, 2004; Nickeleit et al., Nephrol. Dial. Transplant. 15:324-332, 2000; Randhawa et al., Transplantation 67:103-109, 1999. Given the limited treatment options, there is an urgent need for alternative approaches to protect against BKV reactivation and disease.
JCV also is prevalent worldwide, with about 80% of adults showing serological evidence of JCV infection. Stolt et al., J. Gen. Virol. 84:1499-1504, 2003. Most individuals are infected in childhood, without showing any symptoms. The virus remains latent in the lymphocytes, urogenital tract and brain and can reactivate in the immunocompromised, causing disease syndromes. JCV is the causative agent of progressive multifocal leukoencephalopathy (PML), a fatal degenerative disease affecting brain oligodendroglial cells seen in immunosuppressed AIDS, cancer and organ transplant recipient patients. JCV also is associated with hemorrhagic cystitis and nephritis in kidney transplant recipients.
SV40 is a closely related polyomavirus of simians which also widely infects humans and has been associated with some tumor types. This virus has a high degree of serological cross-reactivity with both BKV and JCV antigens. SV40 is believed to spread through a respiratory or fomite route and to be established as a human pathological agent. Its presumed site of persistence also is the kidney, and other tissues that give rise to SV40-associated tumors (e.g., mesothelioma, lymphoma, osteosarcoma, and certain brain tumors).
The capsid of polyomavirus is largely made up of VP1, VP2 and VP3, with each virion containing 360 copies of VP1. Two cellular epitopes of JCV VP1 have been identified, including the epitope sequences, ILMWEAVTL (JCV VP1p100-108; SEQ ID NO:3; referred to herein as “JC100”) and SITEVECFL (JCV VP1p36-44; SEQ ID NO:6; referred to herein as “JC36”). Du Pasquier et al., J. Neurovirol. 7:318-322, 2001; Du Pasquier et al., J. Virol. 77:11918-11926, 2003; Du Pasquier et al., Brain 127(9):1970-1978, 2004; Du Pasquier et al., J. Virol. 78:10206-10, 2004; Koralnik et al., J. Immunol. 168:499-504, 2002; Koralnik et al., J. Virol. 75:3483-3487, 2001. CTL recognizing these epitopes have been associated with control of the virus; patients suffering from the JCV syndrome, progressive multifocal leukoencephalopathy, demonstrate a prolonged survival when they possess CTL responses to the JC100 epitope. Du Pasquier et al., Brain 127(9):1970-1978, 2004; Koralnik et al., J. Immunol. 168:499-504, 2002. BKV-specific cells also have been detected in samples from renal transplant patients. Comoli et al., Transplantation 78:1229-1232, 2004. These prior studies, which used BKV-infected cell lysates as antigens, did not identify any specific antigens or epitopes, however. BKV-specific T-cell lines have been developed from healthy seropositive individuals and kidney transplant recipients. Comoli et al., Transplantation 78:1229-1232, 2004; Comoli et al., J. Am. Soc. Nephrol. 14:3197-3204, 2003; Drummond et al., J. Med. Virol. 17:237-247, 1985; Drummond et al., J. Med. Virol. 23:331-344, 1987.
Several previous studies have shown that both JCV and BKV are common in most adult populations, but that JCV is less prevalent than BKV. Knowles et al., J. Med. Virol. 71:115-123, 2003; Padgett et al., J. Infect. Dis. 127:467-470, 1973; Taguchi et al., Microbiol. Immunol. 26:1057-1064, 1982. Knowles and colleagues reported 81% seropositivity for BKV and 35% for JCV in a survey of 2,435 sera from 1991. Knowles et al., J. Med. Virol. 71:115-123, 2003. These types of studies are complicated by substantial serological crossreactivities between antibodies to these two human polyomaviruses. Viscidi et al., Clin. Diagn. Lab Immunol. 10:278-285, 2003. However, antibody adsorption studies show that some individuals experience infection by both JCV and BKV. This is further supported by PCR studies of polyomavirus shedding in urine that indicate co-infection in a minority of patients. Bendiksen et al., J. Gen. Virol. 81:2625-2633, 2000; Hamilton et al., J. Clin. Microbiol. 38:105-109, 2000; Priftakis et al., J. Clin. Microbiol. 38:406-407, 2000; Shah et al., J. Infect. Dis. 176:1618-1621, 1997.
Knowledge of specific MHC—I restricted epitopes within BK virus antigens allows one to track virus-specific CTLs in at-risk patients and produce compositions to modify immunity to BK and related viruses such as JCV and SV40. Peptides identified as immunoreactive are useful for vaccines as well as diagnostic reagents. Vaccine peptides from viral proteins may be used for enhancing the immune system of mammals with respect to the virus in both seropositive and seronegative individuals. However, no such specific information concerning BKV epitopes has been available. There is a need in the art for compositions and methods which can be used to identify and diagnose polyomavirus-related conditions in patients and patient-derived samples, and to modify the immune response of patients in need, such as immunosuppressed patients, or any person at risk for polyomavirus infection or reactivation.